相关论文: RISMiCal: A software package to perform fast RISM/…
The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However,…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
Path Integral Molecular Dynamics (PIMD) is a well established simulation technique to compute exact equilibrium properties for a quantum system using classical trajectories in an extended phase space. Standard PIMD simulations are…
This paper presents RDCSim, an interactive simulator for reaction--diffusion chemistry (RDC) research, being developed as part of an ongoing project studying how humans interact with unconventional computing systems. While much research…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Solvent can occupy up to ~70% of macromolecular crystals and hence having models that predict solvent distributions in periodic systems could improve in the interpretation of crystallographic data. Yet there are few implicit solvent models…
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The…
A new open source tool for fluid simulation of multi-component plasmas is presented, based on a flexible software design that is applicable to scientific simulations in a wide range of fields. This design enables the same code to be…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
The phase-field method has become a useful tool for the simulation of classical metallurgical phase transformations as well as other phenomena related to materials science. The thermodynamic consistency that forms the basis of these…
This work introduces MICSim, an open-source, pre-circuit simulator designed for early-stage evaluation of chip-level software performance and hardware overhead of mixed-signal compute-in-memory (CIM) accelerators. MICSim features a modular…
MiMiC is a framework for modeling large-scale chemical processes that require treatment at multiple resolutions. It does not aim to implement single-handedly all methods required to treat individual subsystems, but instead, it relegates…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
Integral equation theory of molecular liquids based on statistical mechanics is quite promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. Beginning with a molecular interaction…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…